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rs249707000 SNP Detail
Summary
  • ID
    rs249707000
  • Variation Type
    SNP
  • Alleles
    C/T
Genome Location and Flanking Sequence
  • Location
    Chr1:87054204 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                CACCTTCCTT CATCCTCTCT
GACCACAGGT GATCCTTGGT GGGGGCCGAA AATACATGTT TCCTGCTGGA ACCCCAGACC
CCGAGTATCC AAATGATGCT AATGAGACTG GAACCAGATT GGATGGCAGG AATCTGGTGC
AGGAATGGCT GTCAAAGCAC CAGGTGACCG ACTGCAGAAT ATTAGTGATA CAGTGGAGAC
Y
AGGGAAGGGC TTTGGACCTT ACCAGTTGCT TATGTCCCTC TAGGGATCCC AGTATGTTTG
GAATCGTGAA CAACTCATTC AGAAGGCCCA GGATCCGTCA GTGACATACC TCATGGGTAA
TGGCCCCACA CTTCCTGCAC TGGTACACCT CACATGGCAA CCACTGATCC TCTGTGTATA
TATGTACCGT GACCCCACTG                                            

Y = C/T

    Note: Sequence in lower case indicates low-complexity or repetitive sequence
    BLAST SNP flanking sequence against the mouse Genome
SNP Assays
and
SNP Consensus
Strain alleles of submitted assays, and consensus values for this SNP
Legend
Assay ID Submitter
SNP ID		 Submitter
Handle		 Population
ss orientation
 Variation Type
129P2/OlaHsd
129S1/SvImJ
129S5/SvEvBrd
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C3H/HeH
C3H/HeJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CAST/EiJ
CBA/J
CE/J
CZECHII/EiJ
DBA/1J
DBA/2J
FVB/NJ
I/LnJ
JF1/MsJ
KK/HlJ
LEWES/EiJ
LG/J
LP/J
MA/MyJ
MOLF/EiJ
NOD/ShiLtJ
NON/ShiLtJ
NZB/BlNJ
NZO/HlLtJ
NZW/LacJ
PL/J
PWK/PhJ
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
ss350380311 MGP_WTSI_1_89023057 EVA_MGPV3 EVA_MGPV3 f SNP C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C
SNP Consensus Information
SNP Consensus Type
129P2/OlaHsd
129S1/SvImJ
129S5/SvEvBrd
A/J
AKR/J
B10.RIII-H2 H2-T18/(71NS)SnJ
BALB/cByJ
BALB/cJ
BTBR T<+> Itpr3/J
BUB/BnJ
C3H/HeH
C3H/HeJ
C57BL/6J
C57BL/6NJ
C57BL/10J
C57BL/10SnJ
C57BR/cdJ
C57L/J
C58/J
CAST/EiJ
CBA/J
CE/J
CZECHII/EiJ
DBA/1J
DBA/2J
FVB/NJ
I/LnJ
JF1/MsJ
KK/HlJ
LEWES/EiJ
LG/J
LP/J
MA/MyJ
MOLF/EiJ
NOD/ShiLtJ
NON/ShiLtJ
NZB/BlNJ
NZO/HlLtJ
NZW/LacJ
PL/J
PWK/PhJ
QSi3/Ianm
QSi5/Ianm
RF/J
RIIIS/J
SEA/GnJ
SJL/J
SM/J
SPRET/EiJ
ST/bJ
SWR/J
WSB/EiJ
ZALENDE/EiJ
rs249707000 SNP C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C
Additional submitted assays for this SNP, where the strain of origin for observed alleles is not specified by the submitter
Assay ID Submitter
SNP ID		 Submitter
Handle		 Population
ss orientation
 Variation
Type		 Alleles
ss350380311 MGP_WTSI_1_89023057 SC_MOUSE_GENOMES SC_MOUSE_GENOMES f SNP C/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr1:87054204 () rs orientation: forward
Symbol Name Transcript Protein Function
Class		 Allele Residue Codon
Position		 AA
Position
Akp3 alkaline phosphatase 3, intestine, not Mn requiring within coordinates
Cpgi518 CpG island 518 628 bp proximal
Rr17963 regulatory region 17963 397 bp proximal
Tssr145 transcription start site region 145 130 bp downstream
Tssr146 transcription start site region 146 1106 bp upstream
Tssr147 transcription start site region 147 1458 bp downstream
Tssr7781 transcription start site region 7781 1522 bp downstream
Tssr7782 transcription start site region 7782 1079 bp downstream
Tssr7783 transcription start site region 7783 786 bp downstream
Tssr7784 transcription start site region 7784 544 bp downstream
Tssr7785 transcription start site region 7785 505 bp downstream
Tssr7786 transcription start site region 7786 478 bp downstream
Tssr7787 transcription start site region 7787 149 bp downstream
Tssr7788 transcription start site region 7788 243 bp upstream
Tssr7789 transcription start site region 7789 273 bp upstream
Tssr7790 transcription start site region 7790 327 bp upstream
Tssr7791 transcription start site region 7791 451 bp upstream
Tssr7792 transcription start site region 7792 479 bp upstream
Tssr7793 transcription start site region 7793 492 bp upstream
Tssr7794 transcription start site region 7794 509 bp upstream
Tssr7795 transcription start site region 7795 535 bp upstream
Tssr7796 transcription start site region 7796 558 bp upstream
Tssr7797 transcription start site region 7797 575 bp upstream
Tssr7798 transcription start site region 7798 612 bp upstream
Tssr7799 transcription start site region 7799 848 bp upstream
Tssr7800 transcription start site region 7800 867 bp upstream
Tssr7801 transcription start site region 7801 926 bp upstream
Tssr7802 transcription start site region 7802 1053 bp upstream
Tssr7803 transcription start site region 7803 1114 bp upstream
Tssr7804 transcription start site region 7804 1138 bp upstream
Tssr7805 transcription start site region 7805 1212 bp upstream
Tssr7806 transcription start site region 7806 1226 bp upstream
Tssr7807 transcription start site region 7807 1246 bp upstream
Tssr7808 transcription start site region 7808 1351 bp upstream
Tssr7809 transcription start site region 7809 1421 bp upstream
Tssr7810 transcription start site region 7810 1446 bp upstream
Tssr7811 transcription start site region 7811 1475 bp upstream
Tssr7812 transcription start site region 7812 1525 bp upstream
Tssr7813 transcription start site region 7813 1566 bp upstream
Tssr7814 transcription start site region 7814 1596 bp upstream
Tssr7815 transcription start site region 7815 1664 bp upstream
Tssr7816 transcription start site region 7816 1704 bp upstream
Tssr7817 transcription start site region 7817 1716 bp upstream
Tssr7818 transcription start site region 7818 1891 bp upstream
Tssr12838 transcription start site region 12838 752 bp upstream
Tssr12839 transcription start site region 12839 742 bp upstream
Tssr12840 transcription start site region 12840 733 bp upstream
Tssr12841 transcription start site region 12841 316 bp downstream
Tssr12842 transcription start site region 12842 642 bp downstream
Tssr12843 transcription start site region 12843 904 bp downstream
Tssr12844 transcription start site region 12844 1095 bp downstream
Tssr12845 transcription start site region 12845 1266 bp downstream
Tssr12846 transcription start site region 12846 1327 bp downstream
Tssr12847 transcription start site region 12847 1798 bp downstream
Tssr12848 transcription start site region 12848 1867 bp downstream
Tssr12849 transcription start site region 12849 1886 bp downstream
Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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Send questions and comments to User Support. 		last database update
12/10/2024
MGI 6.24 		The Jackson Laboratory